* samtools-0.1.5-26 (r442)

[samtools.git] / bam_pileup.c

diff --git a/bam_pileup.c b/bam_pileup.c
index d2d2aa6a8f1890b22344d330d0ca7e612c93b244..983c08e6411623da1e322fd071859be4a0af5c3a 100644 (file)
--- a/bam_pileup.c
+++ b/bam_pileup.c
@@ -166,9 +166,13 @@ int bam_plbuf_push(const bam1_t *b, bam_plbuf_t *buf)
                if (b->core.flag & buf->flag_mask) return 0;
                bam_copy1(&buf->tail->b, b);
                buf->tail->beg = b->core.pos; buf->tail->end = bam_calend(&b->core, bam1_cigar(b));
-               if (!(b->core.tid >= buf->max_tid || (b->core.tid == buf->max_tid && buf->tail->beg >= buf->max_pos))) {
-                       fprintf(stderr, "[bam_pileup_core] the input is not sorted. Abort!\n");
-                       abort();
+               if (b->core.tid < buf->max_tid) {
+                       fprintf(stderr, "[bam_pileup_core] the input is not sorted (chromosomes out of order)\n");
+                       return -1;
+               }
+               if ((b->core.tid == buf->max_tid) && (buf->tail->beg < buf->max_pos)) {
+                       fprintf(stderr, "[bam_pileup_core] the input is not sorted (reads out of order)\n");
+                       return -1;
                }
                buf->max_tid = b->core.tid; buf->max_pos = buf->tail->beg;
                if (buf->tail->end > buf->pos || buf->tail->b.core.tid > buf->tid) {